A detailed study of the lipid composition of sedimentary and water particulate samples of a dilute alkaline lake (Santa Olalla Lagoon, Guadalquivir Delta, southwestern Spain) has allowed the identification and quantitation of about 300 compounds reflecting predominant inputs of organic matter and very early diagenetic processes. These lipids, dominated by fatty acids (80-86%), account for up to 0.25% wt. of dry sediment which is consistent with the high eutrophic conditions of the lagoon and suggests a good preservation of the originally produced organic matter. However, the primary lipid compounds, mainly from cyanobacterial origin, are strongly modified. The C30-C32, 1,13- and 1,15-diols constitute the only major group that can be attributed directly to these organisms. The predominant lipids, including the fatty acids, are indicative of intense microbial reworking, namely contributions from gram-positive and gram-negative eubacteria and methanogens. Conversely, the higher plant lipids are better preserved and dominate the aliphatic hydrocarbon fraction. Hydrogenation and dehydration are two major transformation processes in te sedimentary system being reflected in the transformation of sterols into 5-alpha (H)- and 5-beta (H)-stanols and sterenes, and 17-beta (H),21-beta (H)-hopan-22-ol into diploptene. Oxidation in the water column seems to involve the partial transformation of sterols into steroid ketones, phytol into 5,9,13-trimethyltetradecanoic acid and two isomeric 3,7,11,15-tetramethyl-17-hexadecanolides, and, possibly, tetrahymanol into gammacer-3-one. Adiantone and bishomohopanoic acid probably result from the partial oxydation of extended polyhydroxyhopanes or the C30-C33 hydroxyhopanes found in the lagoon waters.